Autarchy of the Private Cave

qotd

Bogdan — Mon, 23 Aug 2010 12:07:51 +0000

“The trouble with the world is that the stupid are cocksure and the intelligent are full of doubt.”
— Bertrand Russell

Only marginally related: Dunning-Kruger effect

DreamPie: the ultimate Python shell

Bogdan — Wed, 11 Aug 2010 14:54:40 +0000

DreamPie: the Python shell you’ve always dreamt about!

• Type your code in the lower pane of the window. To execute, press Ctrl+Enter. One-liners can be executed by simply pressing Enter; If you don’t want them executed, press Space and then Enter.

• Use Ctrl+Up and Ctrl+Down to navigate between code segments you’ve already executed. You can write a few letters before pressing Ctrl+Up, and DreamPie will only search through code segments starting with those letters.

• Press Tab or Ctrl+Space to show a list of completions to the current expression. It will also complete file names!

• Your results are stored in variables named _0, _1, and so on.

• Type a function name and press the space key and DreamPie will automatically add parentheses for you!

Tools for conversion of IDs in genomics

Bogdan — Tue, 10 Aug 2010 12:31:44 +0000

Tools for conversion of IDs in genomics

Recommended: On Basilisk Station (by David Weber)

Bogdan — Sun, 08 Aug 2010 15:19:40 +0000

I definitely enjoyed this high-quality book. It provides enough details to vividly imagine all the people and events, but that is not the main reason I like it. The main reason is duty (or, to be more precise, military duty, albeit highly civil-oriented). Due to high level of details, some may find this book boring – but not those who can remember all the details of what they’ve ever seen.

I would even call this a heroic novel, as heroism (together with duty, persistence and high morals) best describes the actions of Captain Honor Harrington.

I found both a PDF version here (provided by World Public Library Association), and an audio-book here, although I’m not sure those copies are legitimate (i.e. not pirate copies violating international copyright treaties). Use at your own discretion, or just buy a paperback.

This book happens to be the first in Honor Harrington series. I haven’t yet seen other books or reviews thereof, but this one is definitely worth reading on its own.

Linux: how to label swap partition w/o losing swap UUID

Bogdan — Fri, 16 Jul 2010 12:41:13 +0000

In short: sudo mkswap -L new_swap_label -U old_swap_UUID /dev/sd_swap_device.
If you don’t care about the UUID: just sudo mkswap -L new_swap_label /dev/sd_swap_device.

Step-by-step:

Identify current swap UUID: grep swap /etc/fstab ; you should see a line starting with UUID=b4e6e… – note that UUID; let us assume our UUID is b4e6e5d8-8854-4a3e-8edb-f423ded31e2a
Identify swap partition device. If you are using Debian or Ubuntu, device might have been shown to you when running command #1 as a comment of the form

# /dev/sdX4 none swap sw 0 0

Just to be sure, run cat /proc/swaps (or sudo swapon -s), to be shown something like this:

Filename Type Size Used Priority /dev/sdX4 partition 2104504 0 -1
You can also use partition managers to identify swap device, e.g. sudo fdisk -l. Let us assume our partition device is sdX4.
If that swap partition is in use, you need to disable it first: sudo swapoff /dev/sdX4
Now that you have both the UUID and the device, run
sudo mkswap -L new_swap_label -U b4e6e5d8-8854-4a3e-8edb-f423ded31e2a /dev/sdX4
Do not forget replacing sample values above (label, UUID and device) with your actual values.
Enable swap: sudo swapon /dev/sdX4

Now, if you wish so, you may proceed to edit /etc/fstab and replace UUID=…. with LABEL=your_new_swap_label, leaving all other spaces and values in that line untouched.

Analysis of the HDD failures in a large population of hard disks

Bogdan — Sat, 19 Jun 2010 00:16:37 +0000

Will be useful to anyone dealing with more than 1 piece of computer hardware: Disk failures in the real world: What does an MTTF of 1,000,000 hours mean to you?

To get the essence quickly – just scan the tables and figures, and read conclusions.

You might want to read what google engineers tell about HDD failures.

Вірний переклад українською терміну microarray (post in Ukrainian)

Bogdan — Wed, 26 May 2010 12:12:07 +0000

Викладену нижче власну позицію вважаю найправильнішою (і використовую з 2007 року).

Префікс мікро в українській мові є, і позначає певну кратність (10^-6) числової величини (а також просто щось маленьке) – тому його можна зберегти при перекладі першої половини складного слова microarray. Цей префікс також входить до системи одиниць СІ.

А от слова арей (як вживають деякі автори) в українській мові немає. Також немає сенсу його запозичувати, оскільки існують переклади (слова-еквіваленти). Один зі словників пропонує такі варіанти перекладу слова array українською (у різних контекстах):

множина, набір, комплект
розташування, решітка, сітка
масив, список, поле, ряд
решітка даних
масив даних
матриця

Я пропоную використовувати термін мікромасив (та похідний від нього мікромасив-експеримент). Цей термін має перевагу над вживаним у Російській Федерації “микрочип-экспериментом”, оскільки “мікрочіп” або просто “чіп” – це усталений термін електроніки, де він позначає кремнієвий електронний елемент з високим ступенем упаковки напівпровідників; натомість “масив” – це і набір/список [даних], и [двомірна] матриця [даних/ознак/зондів/будь-чого]. Відповідно, мікромасив – це маленька матриця або маленький набір [олігонуклеотидних/кДНК зондів]. Додатковим аргументом проти використання слова чіп вважаю його запозиченість.

Використання інших варіантів перекладу слова array або не відповідає суті об’єкту, або має неоднозначне трактування. Наприклад, мікроматриця: в молекулярній біології матриця – це ланцюг ДНК, з якого іде синтез, а в ширшому значенні – взагалі будь-яка модель, з якої виготовляють зразки. (Звичайно, слово матриця також є синонімом слова масив у значенні двомірний масив / двомірна матриця, але слово масив не має – наскільки мені відомо – альтернативних трактувань у молекулярній біології). Розглядати інші варіанти перекладу слова array не вважаю за потрібне, оскільки вони ще менш вдалі за матрицю.

Таким чином, вірним перекладом терміну microarray є слово мікромасив.

Everything old is new again: nice summary of realworld-digital integration approaches

Bogdan — Sun, 09 May 2010 16:09:09 +0000

Just found a really nice, “almost interactive” TED talk about digital/real-world interfaces. The ideas aren’t new – they have been around for quite a while, as exemplified both by Sci-Fi movies and several digital implant enthusiasts – but this time it comes with a seemingly-tested implementation, which is – WOW! – both cheap and working. Moreover, here ideas are taken to a level of example applications with functional prototypes – which gives hope to have at least some of those market-ready within 5-10 years

I do find the promise to go open-source somewhat naive, but who knows…

Best Linux software to import still images from a digital camera

Bogdan — Sat, 01 May 2010 22:08:01 +0000

Back in the times when Windows was my OS more than 75% of the time in front of the computer, I really liked a simple photos import utility, supplied for Canon digital still image cameras. It allowed the import of all the new media items (photos and movies) from a camera into a pre-configured location in one click, and it also automatically created date-based directories for new photos. Given the removable media autoplay feature, after connecting the camera it was really a matter of one click (or one button press) to have everything copied.

Today, I decided to have a look at what the FOSS community has to match that simple and useful Canon utility. Here’s my “rating”:

digikam: nice and easy import; supports date-based auto-creation of albums (directories); feature-reach, suitable as a primary images-viewing application; my personal “number one” for now.
f-spot: easy import; has nice date-based photos browser; on import, converts photo filenames to lower case; my second choice, will have a closer look at its features.
gThumb: good import, but haven’t found a way to configure/create target directory during import.
gtkam: unusual interface; while testing, it died once unexpectedly; otherwise easy to use.
picasa: haven’t tried to import with a recent version, but I generally dislike the idea of using software which requires an extra layer to run (wine in this case), unless it is unique. Picasa is not unique, and thus looses (in my opinion) to digikam.

The list of Linux music players with CUE sheet support

Bogdan — Fri, 30 Apr 2010 18:45:02 +0000

Last updated: 2010-05-19

DeaDBeeF (as in 0xDEADBEEF) is an audio player for GNU/Linux systems with X11 (though now it also runs in plain console without X, in FreeBSD, and in OpenSolaris) with CUE sheets support
AudioPlayer51 is a free, open-source, cross-platform audio player written to handle FLAC files and CUE sheets (exclusively). If you don’t use FLAC files and CUE sheets, you won’t find AudioPlayer51 very useful.
Amarok: only for WAV+CUE, doesn’t currently support FLAC+CUE; version 2.3.1 is promised to fully support CUE sheets
Audacious (through the .cue plugin)
QMMP (haven’t tested this one)
XMMS through mp3cue (also untested)

Some extra links:

Up or Out: the Value Apex

Bogdan — Thu, 01 Apr 2010 15:14:12 +0000

Up or Out: Solving the IT turnover crisis is an in-depth analysis of the “best employees quit, mediocre employees stay” paradox, with a focus on the culture of quitting.

Tabachnik-inspired remake of Pink Floyd’s Another Brick in the Wall

Bogdan — Wed, 31 Mar 2010 21:50:33 +0000

Dmitri Tabachnik is the Minister of education in the new (Yanukovych team) government.
He is well-known for his anti-Ukrainian rhetoric and for the denial of everything Ukrainian.

The other day he canceled obligatory Ukrainian language university entrance exams, proving again with his actions that he does intend to enact his phobia of Ukrainian identity.

A social response website tabachnik.net.ua has a number of materials on the perception of Tabachnik’s assignment as a Minister of education. The video below is a nice artistic interpretation of the organic resentment of this assignment.

Support from Volodymyr Lytvyn fraction, the Party of Regions and the Communist party helped Dmitri Tabachnik to stay in the Minister’s seat for a while longer: his removal by the Parliament was short of only 24 votes.

Hopefully, sane representatives will keep pushing for the removal of Tabachnik from the position he should have never been to in the first place.

R tutorial links

Bogdan — Mon, 29 Mar 2010 16:17:31 +0000

R time series tutorial (2010, a website of the “Time Series Analysis and Its Applications: With R Examples” book)
Statistics with R (2007)
R for programmers PDF (2008, 104 pages, linked to from here)
Brief R tutorial (2004)
Statistical computing with R: a tutorial (2004)
An introduction to R (from the official r-project website, should be always up-to-date)
R tutorial (date unknown, definitely newer than 2005)

Good online Python book with code examples

Bogdan — Mon, 01 Mar 2010 18:03:11 +0000

screen mastery with only 3 keyboard shortcuts

Bogdan — Mon, 01 Mar 2010 17:11:57 +0000

screen is a must-use for anyone familiar with SSH sessions; it saves your time by keeping your console apps running even after (an unexpected) disconnect from the remote session.

The easiest way to start with screen is screenie – an interface to screen. To use it, you only need to memorize a single keyboard shortcut: C-a d (Ctrl+a, d). This shortcut detaches (hides) your current screen session, allowing to resume later – either with the help of screenie, or by issuing screen -r command.

After a while, with increased screen (and screenie) usage, you will find it inconvenient detaching every time you need a new screen session. Here comes the second keyboard shortcut: C-a c (Ctrl+a, c), which creates a new window within a current screen session, and switches to it.

Finally, you will find it tiresome detaching to then re-attach to a different screen. C-a “ (Ctrl+a, Shift+’) will display a list of screen windows for you to select and switch to.

Screenie, an excellent beginner’s interface to screen, is no longer needed after you memorize these 3 keyboard shortcuts.

Many will say that this is a bare minimum, and also there is much more to screen than what you present here, and that will be true. However, these 3 shortcuts are sufficient for simple but convenient everyday screen sessions management.

ntfstruncate binary for Debian (resetting NTFS bad clusters counter)

Bogdan — Mon, 01 Mar 2010 16:55:56 +0000

There is an excellent step-by-step instruction on resetting the bad clusters counter of an NTFS partition with linux-ntfs tools. I’ve checked – it works as expected:

Back up important data from partition just in case

Find out size of ‘$Bad’ attribute in $Badclus using ntfsinfo -i 8 partition (partition is for example /dev/sda1). It will be the “Allocated size” value in the “Dumping attribute $DATA (0×80)” (there will be two 0×80 attributes. Only one has an “Allocated size” line). Let us write down (remember) this size as ntfs_size.

Use ntfstruncate partition 8 0×80 ‘$Bad’ 0 to set $Bad’s attribute length to zero.

Use ntfstruncate partition 8 0×80 ‘$Bad’ ntfs_size to set $Bad’s attribute length back to proper value ntfs_size which was recorded in step 2.

Boot into Windows and run chkdsk -f diskname. It will find errors and should fix them.

However, Debian’s ntfsprogs package does not have the ntfstruncate binary.

Here’s how you can easily build one yourself (you may need a few extra packages with build tools for that):

apt-get source ntfsprogs
cd linux-ntfs-2.0.0
./configure && make extra
cd ntfsprogs && ./ntfstruncate

You can also install ntfstruncate system-wide, but I have no idea if that will interfere with the already-installed ntfsprogs package, so I just used this binary directly from linux-ntfs-2.0.0/ntfsprogs.

Bad clusters happen not only when cloning an NTFS partition between 2 physical hard disk drives. Once, after a brief blackout (with a turned on PC, and not on a UPS), the SMART status of my new HDD started showing 1 ‘Pending sector’. Correspondingly, all the SMART tests (performed with a smartctl utility) reported read errors. To help my HDD examine and fix the problem itself, I performed a write operation to that single unreadable sector, which restored it (and reset the ‘Pending sector’ counter back to zero). It was possible, because not the physical sector itself, but the hidden CRC field had errors after power failure; modern hard drives can detect and fix this kind of errors upon write operations (read operations only mark the sector as ‘pending’, because data read is not consistent with the stored CRC).

However, NTFS partition still had 4096 bytes in ‘bad clusters’. A little research revealed the presence of internal NTFS bad clusters counter, which can be reset following the procedures above.

Had happiness ever creeped up on you?

Bogdan — Mon, 15 Feb 2010 22:08:54 +0000

“We only value what we loose”, they say.

Fortunately, I haven’t lost anything valuable, and don’t plan to. However, I did come to realize that false leads may and actually do obscure some simple happiness bits we fail to notice in our everyday life. Especially when that happiness comes from someone close, someone you literally got used to as to something inseparable from your life – but still fail to give value to.

Take care of your happiness and inner peace – do stop sometimes to thank and praise and value the oh-so-inseparable people around you.

Copyrights note: this is not my image, and I do not know who is the proper copyrights holder. It is used here for illustrative non-profit purposes, with a proper disclaimer. Contact me if you own the copyright and wish this image removed.

R script to filter probesets with log-expression values below the lowest spike-in

Bogdan — Wed, 27 Jan 2010 12:44:02 +0000

Sometimes there is a need to remove all the probesets, which have expression values below the minimal spike-in intensity on the Affymetrix microarray. The reasoning behind this procedure is simple: minimal-expression spike-ins represent the bottom margin of microarray sensitivity, and anything below that margin cannot be reliably quantified - which also means that both fold-change and p-value of expression variance will be unreliable for these probesets.

Here's a simple R script to do just that. It is abundantly commented, and also contains an optional (commented out) fragment which allows the removal of more low-variance, low-intensity probesets.

Hint: click the "plain text" box header to be able to right-click the code, "Select All", and then "Copy".

PLAIN TEXT

CODE:

filter_below_spikes = function(eset) {
# Finds max(lowest) AFFX/spike-in intensity, and removes rows consisting entirely of values below max(lowest).
# @param eset
# ExpressionSet
# @returns
# exprs(ExpressionSet), filtered
# Without Biobase exprs() will not work.
require(Biobase)
expr = exprs(eset)
# 'expr' sample:
# 1
# 1367452_at 10.880208
# 1367453_at 10.554647
cat(nrow(expr), "rows before filtering.\n")
# Make a vector of spike row names.
spikes = grep("AFFX", rownames(expr), value = TRUE)
cat("Expression matrix has", length(spikes), "spike-in rows.\n")
cat("Summary of spike-in values distribution follows:\n")
print(summary(expr[spikes, ]))
# Find max(lowest) spike-in values.
minval_max = max(as.double(substr(grep("Min", summary(expr[spikes, ]), value = TRUE), 10, 14)))
cat("max(minimal spike-in log-intensity values) =", minval_max, "\n")
# Remove spike-ins from expr.
expr = expr[grep("AFFX", rownames(expr), value = TRUE, invert = TRUE), ]
nospike_rows = nrow(expr)
cat(nospike_rows, "rows remaining after the removal of", length(spikes), "spike-in probesets.\n")
# Optional: calculate max(SD) of all removed rows.
#bad_sds_max = max(apply(expr[!apply((expr> minval_max), 1, any),], 1, sd))
# Now remove all rows, where each value is <= minval_max.
expr = expr[!apply((expr <= minval_max), 1, all), ]
cat(nrow(expr), "rows remaining after filtering out", nospike_rows - nrow(expr), "probesets with all values below", minval_max, "\n")
#cat(bad_sds_max, "is max(SD) of all", nospike_rows - nrow(expr), "filtered probesets with all values below", minval_max, "\n")
# Optional: Remove *some* of the rows, which have at least one value below minval_max, and row_SD <= bad_sds_max.
#pre_final_rows = nrow(expr)
#expr = expr[(apply(expr, 1, sd)> bad_sds_max) | (apply(expr, 1, min)> minval_max), ]
#cat(pre_final_rows-nrow(expr), "rows with SD <=", bad_sds_max, "and min(row) <=", minval_max, "were removed.\n")
#cat(nrow(expr), "final rows returned.\n")
return(expr)
}

Sample use:

> source("script.R")
> expr.filtered = filter_below_spikes(eset)

Comments and suggestions are welcome.

Chandler 1.0.3 package for Debian testing amd64

Bogdan — Mon, 25 Jan 2010 08:52:26 +0000

Recently, I have come across the Chandler project. Chandler is a sophisticated organizer, including tasks, calendar, appointments, invitations, and many more.

The project does provide a 64-bit package for Ubuntu 8.10 "Intrepid Ibex", but it has a dependency on python-zope-interface - which in Debian testing is a virtual package, currently provided by python-zope.interface. That single dependency made my aptitude complain all the time, so I edited the .deb-file, renaming depends/python-zope-interface to depends/python-zope.interface (following nice and simple instructions). After that - no more aptitude complaints, and Chandler works fine.

Download the modified Chandler 1.0.3 Debian testing amd64 package (md5: 239071715977bea2eb75f3bb54491a02).

Standard deviation and variance in pictures

Bogdan — Sun, 24 Jan 2010 14:07:42 +0000

MathIsFun offers nicely illustrated pages on math, algebra, geometry and maybe more.

For example, there is a step-by-step instruction on calculating variance and standard deviation for a set of measured dog heights, with a final picture (below) illustrating one-sigma distance from the mean. Unfortunately, concepts of normal distribution and %% of data points within each sigma range are not discussed, but that might as well be too much for a nice explanation. There are also animations, like this mean machine. Overall, MathIsFun is a nice resource for younglings.

Simple and efficient Drupal upgrades: patch!

Bogdan — Sun, 03 Jan 2010 13:50:37 +0000

Just a quick note: upgrading Drupal using a patch file is a really efficient and fast method, especially because diff/patch files are available for different Drupal version combinations.

Does Google attack your servers, too?

Bogdan — Sat, 05 Dec 2009 12:28:34 +0000

For about 2 weeks now, I am every day alerted of the suspicious behavior of some computer/server from the Google's IP range:

Dec 5 05:39:33 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[option]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:33 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[Itemid]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:33 mx suhosin[3701]: ALERT - tried to register forbidden variable 'GLOBALS' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:33 mx suhosin[3701]: ALERT - ASCII-NUL chars not allowed within request variables - dropped variable 'mosConfig_absolute_path' (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[option]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[Itemid]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - tried to register forbidden variable 'GLOBALS' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - ASCII-NUL chars not allowed within request variables - dropped variable 'mosConfig_absolute_path' (attacker '66.249.71.20', file 'html/index.php')

These requests repeat up to several hundred times per hour, with periods of no or very little malicious requests.

Here's WHOIS information about 66.249.71.20:

OrgName: Google Inc.
OrgID: GOGL
...
NetRange: 66.249.64.0 - 66.249.95.255
CIDR: 66.249.64.0/19
NetName: GOOGLE
NetHandle: NET-66-249-64-0-1
Parent: NET-66-0-0-0-0

Does Google attack you, too?

These attacks initially started from a different Google IP - 66.249.71.2; I wrote to abuse at google, and got an automated response with the ticket number (in the hundreds of millions range). A week after that, requests started flowing from IP 66.249.71.20. I am not inferring "evil Google abuse department" here, just that there was no response, and the problem shifted to a different IP from the Google's IP range.

Update: I decided just to ignore this class of problems.

"Evil?" image by copyblogger.com.

fail2ban and Google translate: how to easily cut your WP blog traffic

Bogdan — Sat, 14 Nov 2009 00:11:08 +0000

fail2ban has a php-url-fopen rule.

WordPress has a Global Translator plugin, which - among others - uses Google Translate service.

If someone uses Google Translate (e.g. using Global Translate's mini-language-flags), and goes back to your blog - that someone might get banned by fail2ban (especially if you have set maxretry to 1), as the referrer will contain the php-URL-fopen attack signature. The bad thing is that you will not realize that until after you check one or several translations yourself, as a random site visitor experiencing the problem is highly unlikely to bother reporting this problem - especially when your blog's Contact page is also inaccessible.

Clearly, Google Translate is not the only legitimate service which will trigger that rule.

Solution: The only solution I have found is to specify the whitelist regex for the php-URL-fopen rule.

Cloud-based bruteforcing, slowloris, and Golang: links

Bogdan — Fri, 13 Nov 2009 16:34:51 +0000

A nice report on the cost of bruteforcing variable-length and variable-complexity passwords using cloud computing services (e.g. Amazon's EC). There's a kind of a tutorial in their previous post.

Slow DoS attack with just 1 computer against a number of web servers, including Apache: slowloris. There is a solution for Apache, packaged for RedHat and also available for Debian.

Finally, there's Go programming language. The most inspiring promise to me personally is the ease of execution parallelization with language's built-in syntactic constructs. That is something highly desired. Also, I like that it is a compiled language. However, it might be 10%-20% slower than pure C. Let's see how it grows.

ocrodjvu: increase accessibility of your DJVU books

Bogdan — Thu, 05 Nov 2009 07:04:23 +0000

ocrodjvu = OCRopus (tesseract) + DJVU

It is a small command-line tool to easily convert your image-only DJVU files into image+text DJVU files. In Debian testing, there are language packages for (in no specific order) German, English, French, Spanish, Vietnamese, Brasilian Portuguese, Dutch, and Italian. The original tesseract-ocr software includes training data & code, so it should be (at least in theory) easy to add more recognition languages.

Ukraine hit by influenza A/H1N1 (swine flu)

Bogdan — Fri, 30 Oct 2009 22:21:12 +0000

Starting October, 30, there is a 3-week quarantine in all primary and higher bodies of education in Ukraine - to limit the spread of the infection.

A total of 80k people were registered with respiratory infections (not classified by flu type). Several small samples tested for A/H1N1 (which is the cause of swine flu pandemic) indicate that 30-50% of all cases could be swine flu (with other cases being "seasonal flu" - that is, previously known influenza types and subtypes). It is reported that ~37 died since Monday, with symptoms matching those of swine flu. Most of the statistics come from the Western regions of Ukraine, which were the first to face rapid daily temperatures decrease - which could have been the trigger of massive infections.

Today I've seen a number of people in Kyiv's underground railway wearing medical face masks (or just pulling their scarfs up to cover noses). Drug stores were literally stormed for anti-virus medications, immune system stimulators, medical face masks, vitamins, etc.

If not the virus, then panic is definitely in the air. I do not recollect seeing something like that before.

Search and replace in a MySQL table

Bogdan — Tue, 27 Oct 2009 07:37:34 +0000

This query performs a table-wide search-and-repalce:

UPDATE `table_name` SET `table_field` = REPLACE(`table_field`,'string to search for and replace','replacement string');

If you need a database-wide search-and-replace, you could try this script (I haven't tested/used it myself).

Beware of the following gotchas:

wrong query syntax may ruin the field you are performing replace on, so always backup first!
be sure to provide "search-for" string as specific as possible, or you will get unexpected replacements (e.g. replacing mini with little will also convert all minivans into littlevans); also, do use WHERE clause when necessary to limit the number of rows modified
the function in the example is case-sensitive, so replacing all minivans with vehicles won't replace Minivans. However, I believe there exists a case-insensitive version of REPLACE function

Configuring web-server: for production and for development

Bogdan — Sun, 25 Oct 2009 15:16:10 +0000

Production: see http://www.howtoforge.com/how-to-set-up-apache2-with-mod_fcgid-and-php5-on-debian-etch - it is for Debian Etch (which is old-stable), but many of the steps apply equally well to Debian Lenny (current-stable). Also, this is a very basic guide, as if you are going to host multiple sites from multiple clients, you most definitely will need some hosting control panel.

Development: see http://www.ruzee.com/blog/2009/01/apache-virtual-hosts-a-clean-setup-for-php-developers. This setup works very well, unless you need to create several virtual hosts every day - in which case necessary actions could be partially scripted.

R under Debian testing/i386: permanently set pdfviewer option

Bogdan — Wed, 21 Oct 2009 14:06:37 +0000

If you get this message when opening vignettes:

Error in openPDF(vif) :
getOption('pdfviewer') is ''; please use 'options(pdfviewer=...)'

and you are tired of running this command every time:

> options(pdfviewer="okular")

then you should check if your system-wide Renviron file has proper PDF viewer set:

grep -i pdf /etc/R/Renviron

R_PDFLATEXCMD=${R_PDFLATEXCMD-${PDFLATEX-'/usr/bin/pdflatex'}}
R_RD4PDF=${R_RD4PDF-'times,hyper'}
## Default PDF viewer
R_PDFVIEWER=${R_PDFVIEWER-''}

It wasn't in my case.

To set one, either edit the system-wide Renviron (e.g. by editing the R_PDFVIEWER=${R_PDFVIEWER-''} line to look like R_PDFVIEWER=${R_PDFVIEWER-'/usr/bin/xdg-open'} - this will use MIME types to open your preferred PDF viewer), or one of the per-user/per-directory Renviron files to fix this minor annoyance (format is the same, e.g. R_PDFVIEWER=okular ).

Single password for multiple sites is safe to use with PwdHash

Bogdan — Fri, 16 Oct 2009 19:46:23 +0000

PwdHash uses your "single password" to create a site-unique password (by making a one-way hash of your password and the site's domain).

Although I'm not using "single password for all sites", PwdHash does look very convenient.